RetrogeneDB ID: retro_pabe_2899

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:108925092..108925351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TRAPPC6A
• Ensembl ID: ENSPPYG00000010109
• Aliases: None
• Description: trafficking protein particle complex 6A [Source:HGNC Symbol;Acc:23069]

Sequence

>retro_pabe_2899
TCCGTGAGGGGACAGAAGATAAGCCTGTTGATCCTGGAGAGTATGGATTTCTGTGTGAGCCAGGTTCTAGGTGAGAGACT
GCTGCTGGAGATGCTCGTCTCAGGGAGGAGCTGGGTGTCCTCAAGTTCATATGCAAAAATCTGTGGACGGCTGTGTTCCA
ATAGAAGGACAGCTTGTGCACCAATCACCAAGGGACCTACTTTTTGCAGGACAACAGCTTCTACTCCTCATCCCAATGAT
CTTGGGCCTGGATTCACTT

Alignment

ORF - retro_pabe_2899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 51.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATKGQKMSLSVLEGMGFRVGQALGERLPREMLA-FREELDVLKFLCKDLWVAVFQKQMDSLRTNHQGTYV
          ...GQK.SL..LE.M.F.V.Q.LGERL..EML...REEL.VLKF.CK.LW.AVFQ...DSL.TNHQGTY.
Retrocopy SVRGQKISLLILESMDFCVSQVLGERLLLEMLV<LREELGVLKFICKNLWTAVFQ*K-DSLCTNHQGTYF

Parental  LQDNSF-PLLLPMASGLQYL
          LQDNSF..LL.PM..GL..L
Retrocopy LQDNSF<LLLIPMILGLDSL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.98 RPM
SRP007412_cerebellum	0.00 RPM	2.19 RPM
SRP007412_heart	0.00 RPM	1.54 RPM
SRP007412_kidney	0.00 RPM	15.51 RPM
SRP007412_liver	0.00 RPM	6.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2899 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2899 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012869	1 retrocopy	retro_cjac_2364,
	ENSG00000007255	0 retrocopies
Macaca mulatta	ENSMMUG00000022932	1 retrocopy	retro_mmul_686,
Pongo abelii	ENSPPYG00000010109	1 retrocopy	retro_pabe_2899 ,